Sun Oct 9 11:15:02 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:15:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 !!! WARNING: HIR 213 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6394942 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -13.99400 41.67500 ymin,ymax (A): -25.35800 30.17000 zmin,zma (A): -18.79600 35.93900 x,y,z range (A): 55.66900 55.52800 54.73500 scale (grids/A): 0.6394942 object centre (A): 13.84050 2.406000 8.571500 number of atom coordinates read : 2908 total number of charged atoms : 2827 net assigned charge : 4.014020 assigned positive charge : 435.8979 centred at (gu) : 90.92463 89.52150 89.13400 assigned negative charge : -431.8857 centred at (gu) : 91.00241 89.40356 89.07730 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8356 nv = 96 ne = 84 npr = 55675 no. pairs analyzed = 55675 no. exposed pairs = 4124 no. arc points = 29304 no. surface atoms = 1369 nbur = 1539 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 516 mr = 4279 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3500000 number of dielectric boundary points 4552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2815 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6090307E-09 1.1000052E-08 midg,1,midg; midg,igrid,midg -1.0306205E-08 1.8858554E-08 1,midg,midg; igrid,midg,midg 1.3037435E-08 -4.9860196E-09 gauss-seidel spectral radius is 0.9873783 estimated iterations to convergence 73 setup time was (sec) 0.6900000 now iterating at: 11:15:03 rms-change max change #iterations 0.1516342 28.44704 at 10iterations 1.5111717E-02 2.494911 at 20iterations 1.6127720E-03 0.2168446 at 30iterations 2.3537378E-04 3.2983780E-02 at 40iterations 5.4355991E-05 7.1172714E-03 at 50iterations finished qdiffx linear iterations at : 11:15:08 total time elapsed so far: 5.420000 # loops : 50 mean,max change (kT/e) : 5.4355991E-05 7.1172714E-03 energy calculations done at 5.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.600000 DelPhi exited at 11:15:09 5.600u 0.462s 0:06.40 94.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:15:09 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 !!! WARNING: HIR 213 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918483 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -13.99400 41.67500 ymin,ymax (A): -25.35800 30.17000 zmin,zma (A): -18.79600 35.93900 x,y,z range (A): 55.66900 55.52800 54.73500 scale (grids/A): 1.918483 object centre (A): 13.84050 2.406000 8.571500 number of atom coordinates read : 2908 total number of charged atoms : 2827 net assigned charge : 4.014020 assigned positive charge : 435.8979 centred at (gu) : 92.77295 88.56344 87.40122 assigned negative charge : -431.8857 centred at (gu) : 93.00723 88.21080 87.23184 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 90327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29304 grid for indexing accessible points = 1.400000 m= 32200 mr = 60442 m= 5458 mr = 22441 m= 331 mr = 3258 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 42087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22270 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6394942 object centre at (A) : 13.84050 2.406000 8.571500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1356208E-02 8.2346071E-03 midg,1,midg; midg,igrid,midg 1.1407578E-02 5.1848553E-02 1,midg,midg; igrid,midg,midg 6.5102619E-03 -9.1139954E-03 gauss-seidel spectral radius is 0.9987150 estimated iterations to convergence 221 setup time was (sec) 1.140000 now iterating at: 11:15:10 rms-change max change #iterations 4.635775 219.4436 at 10iterations 2.204490 65.87796 at 20iterations 1.055928 33.40759 at 30iterations 0.5041606 14.52283 at 40iterations 0.2405839 7.401657 at 50iterations 0.1147039 3.348250 at 60iterations 5.5057343E-02 1.594307 at 70iterations 2.6367698E-02 0.8157997 at 80iterations 1.2649175E-02 0.3477468 at 90iterations 6.0716700E-03 0.1778815 at 100iterations 2.9270807E-03 8.4602356E-02 at 110iterations 1.4107564E-03 4.1755676E-02 at 120iterations finished qdiffx linear iterations at : 11:15:23 total time elapsed so far: 13.55000 # loops : 120 mean,max change (kT/e) : 1.4107564E-03 4.1755676E-02 energy calculations done at 13.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 11:15:23 13.721u 0.564s 0:14.57 98.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:15:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2908 !!! WARNING: HIR 213 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.877724 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -13.99400 41.67500 ymin,ymax (A): -25.35800 30.17000 zmin,zma (A): -18.79600 35.93900 x,y,z range (A): 55.66900 55.52800 54.73500 scale (grids/A): 2.877724 object centre (A): 13.84050 2.406000 8.571500 number of atom coordinates read : 2908 total number of charged atoms : 2827 net assigned charge : 4.014020 assigned positive charge : 435.8979 centred at (gu) : 94.15932 87.84494 86.10171 assigned negative charge : -431.8857 centred at (gu) : 94.51093 87.31617 85.84776 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 208821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29304 grid for indexing accessible points = 1.400000 m= 102665 mr = 147406 m= 38071 mr = 81062 m= 9822 mr = 29498 m= 1357 mr = 7035 m= 58 mr = 839 m= 0 mr = 12 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 94942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 22616 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.918483 object centre at (A) : 13.84050 2.406000 8.571500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2268402 0.1558509 midg,1,midg; midg,igrid,midg 0.1481052 0.6162110 1,midg,midg; igrid,midg,midg 3.7426013E-02 6.1690234E-02 gauss-seidel spectral radius is 0.9993026 estimated iterations to convergence 299 setup time was (sec) 2.470000 now iterating at: 11:15:26 rms-change max change #iterations 11.01514 508.7936 at 10iterations 6.663472 152.2306 at 20iterations 3.993480 87.40307 at 30iterations 2.385464 44.69796 at 40iterations 1.416451 27.73931 at 50iterations 0.8381977 16.53163 at 60iterations 0.4948547 8.991959 at 70iterations 0.2913116 5.486971 at 80iterations 0.1714393 3.163555 at 90iterations 0.1005514 1.632156 at 100iterations 5.9087589E-02 0.9411621 at 110iterations 3.4625817E-02 0.5956802 at 120iterations 2.0281263E-02 0.3406439 at 130iterations 1.1879688E-02 0.2095337 at 140iterations 6.9711073E-03 0.1164970 at 150iterations 4.0840050E-03 6.9424629E-02 at 160iterations 2.3977745E-03 3.9623260E-02 at 170iterations 1.4104397E-03 2.2083282E-02 at 180iterations finished qdiffx linear iterations at : 11:15:47 total time elapsed so far: 23.31000 # loops : 180 mean,max change (kT/e) : 1.4104397E-03 2.2083282E-02 energy calculations done at 23.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.48000 DelPhi exited at 11:15:48 23.488u 0.566s 0:24.52 98.0% 0+0k 0+0io 0pf+0w